is.broadpeak FALSE 
read A549-100nM-Dex-12h-p300-Rep1-ENCLB863RVB.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak :  263588 peaks
 263588 peaks are left after cleaning
 A549-100nM-Dex-12h-p300-Rep2-ENCLB841RWL.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak :  324493 peaks
 324493  peaks are left after cleaninghalf.width= reported 
significant measure= p.value 
URI is done
URI is saved at: IDR-A549-100nM-Dex-12h-p300-Rep1-vs-Rep2-uri.sav 
EM is done

EM is saved at: IDR-A549-100nM-Dex-12h-p300-Rep1-vs-Rep2-em.sav 
EM estimation for the following files
A549-100nM-Dex-12h-p300-Rep1-ENCLB863RVB.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak
A549-100nM-Dex-12h-p300-Rep2-ENCLB841RWL.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak
$p
[1] 0.3842544

$rho1
[1] 0.8787402

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-A549-100nM-Dex-12h-p300-Rep1-vs-Rep2-overlapped-peaks.txt
Write number of peaks above IDR cutoff [0.01, 0.25]: npeaks-aboveIDR.txt
Marginal mean of two components:
$x.mean1
[1] 9995.38

$x.mean2
[1] 22928.14

$y.mean1
[1] 9888.302

$y.mean2
[1] 22995.05

$x.sd1
[1] 8621.817

$x.sd2
[1] 7985.995

$y.sd1
[1] 8208.65

$y.sd2
[1] 8147.34